This Article Full Text Full Text (PDF) All Versions of this Article: biophysj.105.078030v1 90/10/3410    most recent Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Hyeon, C. Articles by Thirumalai, D. Search for Related Content PubMed PubMed Citation Articles by Hyeon, C. Articles by Thirumalai, D.

Forced-Unfolding and Force-Quench Refolding of RNA Hairpins

Changbong Hyeon ^* and D. Thirumalai ^* 

^* Biophysics Program Institute for Physical Science and Technology and Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland

Correspondence: Address reprint requests to D. Thirumalai, Tel.: 301-405-4803; E-mail: thirum{at}glue.umd.edu.

Nanomanipulation of individual RNA molecules, using laser optical tweezers, has made it possible to infer the major features of their energy landscape. Time-dependent mechanical unfolding trajectories, measured at a constant stretching force (f_S) of simple RNA structures (hairpins and three-helix junctions) sandwiched between RNA/DNA hybrid handles show that they unfold in a reversible all-or-none manner. To provide a molecular interpretation of the experiments we use a general coarse-grained off-lattice G-like model, in which each nucleotide is represented using three interaction sites. Using the coarse-grained model we have explored forced-unfolding of RNA hairpin as a function of f_S and the loading rate (r_f). The simulations and theoretical analysis have been done both with and without the handles that are explicitly modeled by semiflexible polymer chains. The mechanisms and timescales for denaturation by temperature jump and mechanical unfolding are vastly different. The directed perturbation of the native state by f_S results in a sequential unfolding of the hairpin starting from their ends, whereas thermal denaturation occurs stochastically. From the dependence of the unfolding rates on r_f and f_S we show that the position of the unfolding transition state is not a constant but moves dramatically as either r_f or f_S is changed. The transition-state movements are interpreted by adopting the Hammond postulate for forced-unfolding. Forced-unfolding simulations of RNA, with handles attached to the two ends, show that the value of the unfolding force increases (especially at high pulling speeds) as the length of the handles increases. The pathways for refolding of RNA from stretched initial conformation, upon quenching f_S to the quench force f_Q, are highly heterogeneous. The refolding times, upon force-quench, are at least an order-of-magnitude greater than those obtained by temperature-quench. The long f_Q-dependent refolding times starting from fully stretched states are analyzed using a model that accounts for the microscopic steps in the rate-limiting step, which involves the trans to gauche transitions of the dihedral angles in the GAAA tetraloop. The simulations with explicit molecular model for the handles show that the dynamics of force-quench refolding is strongly dependent on the interplay of their contour length and persistence length and the RNA persistence length. Using the generality of our results, we also make a number of precise experimentally testable predictions.

This article has been cited by other articles:

				C. Hyeon, G. Morrison, and D. Thirumalai Force-dependent hopping rates of RNA hairpins can be estimated from accurate measurement of the folding landscapes PNAS, July 15, 2008; 105(28): 9604 - 9609. [Abstract] [Full Text] [PDF]

				M. Mickler, R. I. Dima, H. Dietz, C. Hyeon, D. Thirumalai, and M. Rief Revealing the bifurcation in the unfolding pathways of GFP by using single-molecule experiments and simulations PNAS, December 18, 2007; 104(51): 20268 - 20273. [Abstract] [Full Text] [PDF]

				O. K. Dudko, J. Mathe, A. Szabo, A. Meller, and G. Hummer Extracting Kinetics from Single-Molecule Force Spectroscopy: Nanopore Unzipping of DNA Hairpins Biophys. J., June 15, 2007; 92(12): 4188 - 4195. [Abstract] [Full Text] [PDF]

				K. A. Walther, F. Grater, L. Dougan, C. L. Badilla, B. J. Berne, and J. M. Fernandez Signatures of hydrophobic collapse in extended proteins captured with force spectroscopy PNAS, May 8, 2007; 104(19): 7916 - 7921. [Abstract] [Full Text] [PDF]

				M. Manosas, J.-D. Wen, P. T. X. Li, S. B. Smith, C. Bustamante, I. Tinoco Jr., and F. Ritort Force Unfolding Kinetics of RNA using Optical Tweezers. II. Modeling Experiments Biophys. J., May 1, 2007; 92(9): 3010 - 3021. [Abstract] [Full Text] [PDF]

				C. Hyeon and D. Thirumalai Mechanical Unfolding of RNA: From Hairpins to Structures with Internal Multiloops Biophys. J., February 1, 2007; 92(3): 731 - 743. [Abstract] [Full Text] [PDF]